Prolog is to Lisp what assembly is to C: used occasionally for specific purposes, where absolutely necessary.
Prolog is a fun language, on it's own, but one feels like his arms have been cut off and his legs made 100 times more powerful when using prolog; it empowers you in some aspects, but completely disables you in others. So, many people opt to get it in a form where it's embedded in Lisp, to augment its shortcomings and exploit its powers.
That's because the design of the language is so strongly skewed towards unification and search. It's great as a database / ruleset query language, for example, but it's not as general-purpose as e.g. Lisp or ML. It makes a lot of sense to embed it in something else. (I wouldn't try to write a web server in Make, either, but Make is quite useful in its specific domain.)
Prolog is a fun language, on it's own, but one feels like his arms have been cut off and his legs made 100 times more powerful when using prolog; it empowers you in some aspects, but completely disables you in others. So, many people opt to get it in a form where it's embedded in Lisp, to augment its shortcomings and exploit its powers.